Shokhirev Maxim N, Johnson Adiv A
Tally Health, New York, NY, USA.
Geroscience. 2025 Aug 11. doi: 10.1007/s11357-025-01824-1.
Using 100 technical replicate samples from two adult buccal cohorts, we compared technical methylation variability and signal strength between the Infinium MethylationEPIC v2.0 array and the Twist Human Methylome Panel across 753,648 shared CpGs. Twist methylation sequencing showed skewed methylation distributions and fewer highly correlated CpGs than MethylationEPIC arrays. Variance analysis revealed a skew toward higher signal strength in MethylationEPIC datasets, with a subset of CpGs showing high signal strength in both methylation sequencing and array datasets. Despite these biases, four principal component (PC) trained epigenetic clocks (pcHorvath1, pcHorvath2, pcHannum, and pcDNAm PhenoAge) were robust across both technologies, even with missing data. While pcHannum and pcDNAm PhenoAge were similarly reproducible with mean absolute replicate difference (MRD) values ranging from 1.014 years to 1.194 years, pcHorvath1 was more reproducible in arrays (MRD = 0.459 years) than methylation sequencing (MRD = 2.320 years) and pcHorvath2 was more reproducible in methylation sequencing (MRD = 0.760 years) than arrays (MRD = 1.011 years). Furthermore, original non-PC versions of these clocks were less reproducible in Twist datasets and, as an example of this, MRD for uncorrected clocks went as high as 15.498 years in arrays and as high as 20.180 years in methylation sequencing. Obvious differences in age prediction were also observed in original clocks compared to their PC-trained versions across both technologies (with a mean absolute difference ranging from 4.492 years to 46.724 years). This underscores the need for careful selection of epigenetic clocks and technology-specific adjustments when optimizing for accuracy and reproducibility.
我们使用来自两个成人颊部队列的100个技术重复样本，比较了Infinium MethylationEPIC v2.0阵列和Twist人类甲基化组面板在753,648个共享CpG位点上的技术甲基化变异性和信号强度。Twist甲基化测序显示甲基化分布存在偏差，且与MethylationEPIC阵列相比，高度相关的CpG位点更少。方差分析显示MethylationEPIC数据集的信号强度倾向于更高，有一部分CpG位点在甲基化测序和阵列数据集中均显示出高信号强度。尽管存在这些偏差，但四个主成分（PC）训练的表观遗传时钟（pcHorvath1、pcHorvath2、pcHannum和pcDNAm PhenoAge）在两种技术中都很稳健，即使存在缺失数据。虽然pcHannum和pcDNAm PhenoAge的平均绝对重复差异（MRD）值在1.014年至1.194年之间，具有相似的可重复性，但pcHorvath1在阵列中的可重复性更高（MRD = 0.459年），而在甲基化测序中的可重复性较低（MRD = 2.320年），pcHorvath2在甲基化测序中的可重复性更高（MRD = 0.760年），而在阵列中的可重复性较低（MRD = 1.011年）。此外，这些时钟的原始非PC版本在Twist数据集中的可重复性较低，例如，未校正时钟在阵列中的MRD高达15.498年，在甲基化测序中的MRD高达20.180年。与两种技术中它们的PC训练版本相比，原始时钟在年龄预测方面也存在明显差异（平均绝对差异范围为4.492年至46.724年）。这强调了在优化准确性和可重复性时，需要仔细选择表观遗传时钟并进行特定技术调整。
